Targeting individual cells by barcode in pooled sequence libraries. Issue 1 (26th September 2018)

• Record Type: Journal Article
• Authors: Ranu, Navpreet; Villani, Alexandra-Chloé; Hacohen, Nir; Blainey, Paul C
• Is Part Of: Nucleic acids research. Volume 47:Issue 1(2019)
• Page Start: e4
• Page End: e4
• Publication Date: 2018-09-26
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gky856
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Transcriptional profiling of thousands of single cells in parallel by RNA-seq is now routine. However, due to reliance on pooled library preparation, targeting analysis to particular cells of interest is difficult. Here, we present a multiplexed PCR method for targeted sequencing of select cells from pooled single-cell sequence libraries. We demonstrated this molecular enrichment method on multiple cell types within pooled single-cell RNA-seq libraries produced from primary human blood cells. We show how molecular enrichment can be combined with FACS to efficiently target ultra-rare cell types, such as the recently identified AXL + SIGLEC6 + dendritic cell (AS DC) subset, in order to reduce the required sequencing effort to profile single cells by 100-fold. Our results demonstrate that DNA barcodes identifying cells within pooled sequencing libraries can be used as targets to enrich for specific molecules of interest, for example reads from a set of target cells.